The development of RNA interference (RNAi) techniques has accelerated our capacity to study knockdown phenotypes and infer the function and mechanism of disease genes [ 10].
Improved annotations allow for better understanding and interpretation of genomic and transcriptomic experiments, including analyzing the functional implications of insertions, deletions, and mutations, inferring the function of understudied genes, and determining functional changes resulting from differential expression studies.
Knowledge of what ligands bind to a protein and where they bind can help in inferring the function.
In practice, it has been successfully applied to large-scale problems of deciphering error-correction codes (Kschischang et al. 2001), inferring the functions of protein DNA and protein protein interactions (Yeang et al. 2004), and determining the causal orders of genes in the regulatory network (Vaske et al. 2009).
Experimental identification of function of one such domain might help in inferring the functions of clustered domains.
To elucidate functional divergence among the Gsdma-related genes in mice, and to infer the function of the human and rat orthologs, we examined in vivo function of mouse Gsdma by generating Gsdma knockout mice and transgenic mice that overexpress wild-type Gsdma or Gsdma harboring a point mutation (Alanine339Threonine).
A reliable identification of interfacial residues is vital not only to infer the function of individual proteins and their assembly into biological complexes, but also to elucidate the molecular and physicochemical basis of interactions between proteins.
It has been applied to gene function prediction, utilizing known gene functions and interactions to infer the function of other genes [ 18].
For instance, protein interaction networks can be used to identify hub proteins having critical biological functions, to predict biological pathways, and to infer the function of a protein according to its interactions with other proteins with known functions [22] [24].
k-nearest neighbor classifiers are used widely and successfully to infer the function of newly sequenced proteins.
